FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: GYQ61

Calculation Name: 1E5R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1E5R

Chain ID: A

ChEMBL ID:

UniProt ID: O09345

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 264
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3733511.092321
FMO2-HF: Nuclear repulsion 3626721.621772
FMO2-HF: Total energy -106789.47055
FMO2-MP2: Total energy -107105.412575


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-22.95-15.21216.413-9.69-14.459-0.085
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.056 / q_NPA : -0.021
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3SER00.0390.0102.740-3.502-0.5950.465-1.562-1.811-0.005
4A4HIS10.7760.8722.336-0.8150.1721.131-0.505-1.6140.001
5A5ILE00.0150.0167.0160.0920.0920.0000.0000.0000.000
6A6LEU0-0.007-0.0045.524-0.072-0.0720.0000.0000.0000.000
7A7GLY00.0350.0219.014-0.039-0.0390.0000.0000.0000.000
8A8LYS10.7890.88312.6680.1540.1540.0000.0000.0000.000
9A9ILE00.0170.04016.0680.0020.0020.0000.0000.0000.000
10A10GLU-1-0.847-0.92319.110-0.114-0.1140.0000.0000.0000.000
11A11LEU0-0.010-0.01021.7310.0000.0000.0000.0000.0000.000
12A12ASP-1-0.810-0.90624.508-0.069-0.0690.0000.0000.0000.000
13A13GLN00.0690.01728.052-0.002-0.0020.0000.0000.0000.000
14A14THR0-0.065-0.03429.7250.0020.0020.0000.0000.0000.000
15A15ARG10.7610.82928.0380.0850.0850.0000.0000.0000.000
16A16LEU00.0270.02725.379-0.001-0.0010.0000.0000.0000.000
17A17ALA0-0.035-0.01729.0780.0010.0010.0000.0000.0000.000
18A18PRO0-0.034-0.01131.7280.0020.0020.0000.0000.0000.000
19A19ASP-1-0.742-0.90728.482-0.076-0.0760.0000.0000.0000.000
20A20LEU0-0.040-0.00626.0230.0000.0000.0000.0000.0000.000
21A21ALA0-0.015-0.00729.4050.0020.0020.0000.0000.0000.000
22A22TYR00.023-0.00230.1060.0040.0040.0000.0000.0000.000
23A23LEU0-0.023-0.01225.3130.0020.0020.0000.0000.0000.000
24A24ALA0-0.0030.00129.1580.0010.0010.0000.0000.0000.000
25A25ALA0-0.056-0.03130.9580.0040.0040.0000.0000.0000.000
26A26VAL0-0.041-0.00729.5580.0030.0030.0000.0000.0000.000
27A27PRO00.015-0.01031.714-0.002-0.0020.0000.0000.0000.000
28A28THR0-0.087-0.02828.046-0.002-0.0020.0000.0000.0000.000
29A29VAL00.002-0.01128.9990.0030.0030.0000.0000.0000.000
30A30GLU-1-0.921-0.96130.121-0.028-0.0280.0000.0000.0000.000
31A31GLU-1-0.933-0.96823.765-0.078-0.0780.0000.0000.0000.000
32A32GLU-1-0.916-0.94126.481-0.042-0.0420.0000.0000.0000.000
33A33TYR0-0.066-0.05525.981-0.003-0.0030.0000.0000.0000.000
34A34ASP-1-0.927-0.95128.011-0.003-0.0030.0000.0000.0000.000
35A35GLU-1-0.879-0.90922.269-0.041-0.0410.0000.0000.0000.000
36A36PHE0-0.066-0.05422.0240.0150.0150.0000.0000.0000.000
37A37SER0-0.006-0.01922.5620.0000.0000.0000.0000.0000.000
38A38ASN0-0.116-0.05723.750-0.002-0.0020.0000.0000.0000.000
39A39GLY00.025-0.00325.575-0.006-0.0060.0000.0000.0000.000
40A40PHE00.0190.02226.920-0.003-0.0030.0000.0000.0000.000
41A41TRP00.0440.01822.843-0.005-0.0050.0000.0000.0000.000
42A42LYS10.8080.90924.1820.0600.0600.0000.0000.0000.000
43A43HIS00.0500.02519.475-0.021-0.0210.0000.0000.0000.000
44A44VAL00.0190.02423.5200.0080.0080.0000.0000.0000.000
45A45PRO0-0.028-0.02022.773-0.007-0.0070.0000.0000.0000.000
46A46LEU00.022-0.05222.4980.0070.0070.0000.0000.0000.000
47A47TRP00.0520.01321.0790.0030.0030.0000.0000.0000.000
48A48ASN0-0.0160.03520.896-0.015-0.0150.0000.0000.0000.000
49A67GLN0-0.018-0.00823.861-0.002-0.0020.0000.0000.0000.000
50A68PRO00.0440.01025.107-0.002-0.0020.0000.0000.0000.000
51A69THR0-0.0110.02925.7950.0050.0050.0000.0000.0000.000
52A70ALA0-0.004-0.00728.201-0.001-0.0010.0000.0000.0000.000
53A71HIS00.0350.01527.7570.0030.0030.0000.0000.0000.000
54A72VAL0-0.0070.00426.0320.0000.0000.0000.0000.0000.000
55A73GLU-1-0.821-0.88728.648-0.074-0.0740.0000.0000.0000.000
56A74HIS0-0.070-0.01531.8440.0030.0030.0000.0000.0000.000
57A75VAL0-0.039-0.01831.359-0.001-0.0010.0000.0000.0000.000
58A76PRO00.0300.01728.919-0.004-0.0040.0000.0000.0000.000
59A77TYR00.1010.08225.099-0.006-0.0060.0000.0000.0000.000
60A78LEU00.035-0.00823.180-0.007-0.0070.0000.0000.0000.000
61A79LYS10.8680.91923.1550.0720.0720.0000.0000.0000.000
62A80GLU-1-0.816-0.83024.212-0.095-0.0950.0000.0000.0000.000
63A81ILE00.0040.01719.746-0.007-0.0070.0000.0000.0000.000
64A82VAL0-0.047-0.04418.396-0.009-0.0090.0000.0000.0000.000
65A83THR0-0.082-0.06519.630-0.003-0.0030.0000.0000.0000.000
66A84THR0-0.073-0.04521.009-0.005-0.0050.0000.0000.0000.000
67A85VAL0-0.015-0.00815.085-0.008-0.0080.0000.0000.0000.000
68A86PHE0-0.004-0.02112.164-0.014-0.0140.0000.0000.0000.000
69A87ASP-1-0.798-0.87914.973-0.151-0.1510.0000.0000.0000.000
70A88GLY0-0.010-0.04815.687-0.003-0.0030.0000.0000.0000.000
71A89THR0-0.109-0.05416.9930.0070.0070.0000.0000.0000.000
72A90HIS00.0590.03611.6770.0190.0190.0000.0000.0000.000
73A91LEU0-0.0250.02314.420-0.006-0.0060.0000.0000.0000.000
74A92GLN0-0.030-0.01814.657-0.004-0.0040.0000.0000.0000.000
75A93MET0-0.001-0.02316.4550.0000.0000.0000.0000.0000.000
76A94ALA00.0100.01216.905-0.011-0.0110.0000.0000.0000.000
77A95ARG10.8420.92118.6140.1240.1240.0000.0000.0000.000
78A96SER00.0390.02819.555-0.008-0.0080.0000.0000.0000.000
79A97ARG10.9070.92815.1790.1710.1710.0000.0000.0000.000
80A98ASN0-0.0100.00220.960-0.003-0.0030.0000.0000.0000.000
81A99LEU00.0040.00119.807-0.001-0.0010.0000.0000.0000.000
82A100LYS10.8550.94723.5110.0410.0410.0000.0000.0000.000
83A101ASN0-0.009-0.00226.5880.0000.0000.0000.0000.0000.000
84A102ALA00.0450.02224.0780.0040.0040.0000.0000.0000.000
85A103ILE0-0.043-0.01619.823-0.002-0.0020.0000.0000.0000.000
86A104VAL00.0150.03116.8880.0000.0000.0000.0000.0000.000
87A105ILE0-0.002-0.00718.0830.0040.0040.0000.0000.0000.000
88A106PRO00.0240.00914.783-0.023-0.0230.0000.0000.0000.000
89A107HIS10.8310.92913.3330.1040.1040.0000.0000.0000.000
90A108ARG10.8860.9609.295-0.372-0.3720.0000.0000.0000.000
91A109ASP-1-0.869-0.9409.793-0.269-0.2690.0000.0000.0000.000
92A110PHE00.0010.0069.5590.0770.0770.0000.0000.0000.000
93A119ARG10.8540.9336.7310.1580.1580.0000.0000.0000.000
94A120TYR0-0.059-0.0547.7960.2110.2110.0000.0000.0000.000
95A121PHE00.016-0.0093.799-0.789-0.3230.054-0.092-0.4280.000
96A122ARG10.8310.9007.4020.1760.1760.0000.0000.0000.000
97A123THR0-0.065-0.0428.4750.0150.0150.0000.0000.0000.000
98A124PHE0-0.021-0.03310.886-0.008-0.0080.0000.0000.0000.000
99A125MET00.0280.03513.3570.0010.0010.0000.0000.0000.000
100A126VAL0-0.0290.00716.3780.0090.0090.0000.0000.0000.000
101A127LEU00.000-0.03118.982-0.001-0.0010.0000.0000.0000.000
102A128GLU-1-0.802-0.86722.286-0.064-0.0640.0000.0000.0000.000
103A129ASP-1-0.912-0.96322.797-0.072-0.0720.0000.0000.0000.000
104A130SER0-0.025-0.00723.1930.0090.0090.0000.0000.0000.000
105A131PRO00.020-0.01223.165-0.002-0.0020.0000.0000.0000.000
106A132LEU0-0.047-0.01823.8490.0030.0030.0000.0000.0000.000
107A133ALA00.0010.01021.0790.0040.0040.0000.0000.0000.000
108A134PHE0-0.040-0.01917.984-0.001-0.0010.0000.0000.0000.000
109A135HIS00.015-0.00413.3690.0080.0080.0000.0000.0000.000
110A136SER0-0.006-0.01013.2150.0160.0160.0000.0000.0000.000
111A137ASN0-0.013-0.0096.3940.1760.1760.0000.0000.0000.000
112A138GLU-1-0.764-0.8546.6001.0951.0950.0000.0000.0000.000
113A139ASP-1-0.877-0.9379.6740.7030.7030.0000.0000.0000.000
114A140THR0-0.052-0.0279.322-0.073-0.0730.0000.0000.0000.000
115A141VAL00.0240.01412.130-0.018-0.0180.0000.0000.0000.000
116A142ILE0-0.025-0.01310.755-0.006-0.0060.0000.0000.0000.000
117A143HIS10.8750.93114.4860.0840.0840.0000.0000.0000.000
118A144MET0-0.0450.00211.901-0.002-0.0020.0000.0000.0000.000
119A145ARG10.8180.88616.2310.1430.1430.0000.0000.0000.000
120A146PRO00.016-0.01518.200-0.013-0.0130.0000.0000.0000.000
121A147GLY00.0390.03119.1050.0020.0020.0000.0000.0000.000
122A148GLU-1-0.809-0.87614.175-0.176-0.1760.0000.0000.0000.000
123A149ILE00.0060.01011.3470.0080.0080.0000.0000.0000.000
124A150TRP0-0.006-0.0318.800-0.039-0.0390.0000.0000.0000.000
125A151PHE00.0270.0242.311-0.5110.9194.348-1.429-4.349-0.011
126A152LEU0-0.066-0.0526.209-0.135-0.1350.0000.0000.0000.000
127A153ASP-1-0.806-0.9011.951-15.211-15.1989.494-5.015-4.492-0.057
128A154ALA00.0300.0124.6100.8010.874-0.001-0.016-0.0550.000
129A155ALA0-0.015-0.0154.5750.4420.498-0.001-0.001-0.0530.000
130A156THR0-0.046-0.0273.5780.1610.4280.008-0.073-0.2020.000
131A157VAL0-0.024-0.0246.428-0.287-0.2870.0000.0000.0000.000
132A158HIS10.7950.9128.2130.3640.3640.0000.0000.0000.000
133A159SER0-0.0220.00210.9940.0310.0310.0000.0000.0000.000
134A160ALA00.004-0.00114.327-0.033-0.0330.0000.0000.0000.000
135A161VAL0-0.014-0.01016.8440.0190.0190.0000.0000.0000.000
136A162ASN00.001-0.01720.376-0.005-0.0050.0000.0000.0000.000
137A163PHE0-0.044-0.02422.0670.0070.0070.0000.0000.0000.000
138A164SER0-0.031-0.00126.2000.0040.0040.0000.0000.0000.000
139A165GLU-1-0.880-0.94227.948-0.027-0.0270.0000.0000.0000.000
140A166ILE0-0.008-0.00827.766-0.003-0.0030.0000.0000.0000.000
141A167SER0-0.063-0.05526.941-0.002-0.0020.0000.0000.0000.000
142A168ARG10.9590.96118.5480.1060.1060.0000.0000.0000.000
143A169GLN00.0320.04922.013-0.015-0.0150.0000.0000.0000.000
144A170SER0-0.013-0.01218.057-0.005-0.0050.0000.0000.0000.000
145A171LEU00.0040.01118.1900.0070.0070.0000.0000.0000.000
146A172CYS0-0.060-0.02114.683-0.011-0.0110.0000.0000.0000.000
147A173VAL00.0600.02914.1420.0140.0140.0000.0000.0000.000
148A174ASP-1-0.700-0.78111.707-0.291-0.2910.0000.0000.0000.000
149A175PHE0-0.028-0.03110.0890.0260.0260.0000.0000.0000.000
150A176ALA0-0.0050.00610.937-0.034-0.0340.0000.0000.0000.000
151A177PHE00.0500.0089.1720.0220.0220.0000.0000.0000.000
152A178ASP-1-0.899-0.93911.054-0.168-0.1680.0000.0000.0000.000
153A179GLY0-0.032-0.04911.9640.0210.0210.0000.0000.0000.000
154A180PRO0-0.118-0.0608.789-0.001-0.0010.0000.0000.0000.000
155A181PHE00.0320.0435.699-0.0080.071-0.001-0.007-0.0700.000
156A182ASP-1-0.814-0.8825.897-1.207-1.2070.0000.0000.0000.000
157A183GLU-1-0.761-0.8652.626-4.657-3.1970.916-0.990-1.385-0.013
158A184LYS10.8350.8975.5421.1221.1220.0000.0000.0000.000
159A185GLU-1-0.896-0.9408.796-0.271-0.2710.0000.0000.0000.000
160A186ILE0-0.0110.0038.2350.0650.0650.0000.0000.0000.000
161A187PHE0-0.039-0.0339.6310.0380.0380.0000.0000.0000.000
162A188ALA00.0290.04213.4080.0010.0010.0000.0000.0000.000
163A189ASP-1-0.851-0.90216.923-0.176-0.1760.0000.0000.0000.000
164A190ALA0-0.012-0.02514.467-0.012-0.0120.0000.0000.0000.000
165A191THR0-0.100-0.07614.784-0.024-0.0240.0000.0000.0000.000
166A192LEU0-0.016-0.01915.5700.0000.0000.0000.0000.0000.000
167A193TYR0-0.121-0.0505.8810.0560.0560.0000.0000.0000.000
168A194ALA00.030-0.01111.8580.0110.0110.0000.0000.0000.000
169A195PRO0-0.007-0.0147.8900.0450.0450.0000.0000.0000.000
170A196GLY0-0.015-0.0029.510-0.012-0.0120.0000.0000.0000.000
171A197SER0-0.039-0.00512.0900.0560.0560.0000.0000.0000.000
172A198THR0-0.004-0.00312.812-0.014-0.0140.0000.0000.0000.000
173A199PRO00.0170.00811.7280.0110.0110.0000.0000.0000.000
174A200ASP-1-0.858-0.91614.282-0.048-0.0480.0000.0000.0000.000
175A201LEU0-0.049-0.03612.317-0.011-0.0110.0000.0000.0000.000
176A202PRO00.001-0.00116.3800.0140.0140.0000.0000.0000.000
177A203GLU-1-0.930-0.94918.9620.0430.0430.0000.0000.0000.000
178A204ARG10.8110.90615.348-0.152-0.1520.0000.0000.0000.000
179A205ARG10.8990.95522.091-0.034-0.0340.0000.0000.0000.000
180A206PRO00.0940.03623.5500.0100.0100.0000.0000.0000.000
181A207PHE00.0260.02022.880-0.015-0.0150.0000.0000.0000.000
182A208THR0-0.018-0.01924.7450.0100.0100.0000.0000.0000.000
183A209ALA00.0870.02827.8900.0010.0010.0000.0000.0000.000
184A210GLU-1-0.846-0.90429.4720.0660.0660.0000.0000.0000.000
185A211HIS00.0410.02326.456-0.007-0.0070.0000.0000.0000.000
186A212ARG10.8060.87923.746-0.156-0.1560.0000.0000.0000.000
187A213ARG10.9220.95528.456-0.075-0.0750.0000.0000.0000.000
188A214ARG10.8110.88331.077-0.068-0.0680.0000.0000.0000.000
189A215ILE00.0060.04225.874-0.006-0.0060.0000.0000.0000.000
190A216LEU00.0250.00828.497-0.004-0.0040.0000.0000.0000.000
191A217SER0-0.052-0.02731.396-0.005-0.0050.0000.0000.0000.000
192A218LEU00.0190.00329.601-0.005-0.0050.0000.0000.0000.000
193A219GLY0-0.003-0.00633.309-0.002-0.0020.0000.0000.0000.000
194A220GLN0-0.103-0.06534.338-0.005-0.0050.0000.0000.0000.000
195A221VAL0-0.032-0.01335.116-0.003-0.0030.0000.0000.0000.000
196A222ILE0-0.055-0.00930.450-0.002-0.0020.0000.0000.0000.000
197A223GLU-1-0.876-0.93034.6920.0310.0310.0000.0000.0000.000
198A224ARG10.8170.85534.305-0.036-0.0360.0000.0000.0000.000
199A225GLU-1-0.900-0.96034.1320.0250.0250.0000.0000.0000.000
200A226ASN0-0.040-0.01033.7560.0000.0000.0000.0000.0000.000
201A227PHE00.0420.00827.2560.0020.0020.0000.0000.0000.000
202A228ARG10.9400.97227.846-0.003-0.0030.0000.0000.0000.000
203A229ASP-1-0.867-0.93927.6330.0180.0180.0000.0000.0000.000
204A230ILE00.000-0.00728.1750.0010.0010.0000.0000.0000.000
205A231LEU00.0450.04021.8770.0060.0060.0000.0000.0000.000
206A232PHE00.0430.01923.5400.0040.0040.0000.0000.0000.000
207A233LEU0-0.065-0.02324.582-0.002-0.0020.0000.0000.0000.000
208A234LEU0-0.003-0.01323.8090.0020.0020.0000.0000.0000.000
209A235SER00.000-0.02220.2050.0100.0100.0000.0000.0000.000
210A236LYS10.9390.97520.056-0.017-0.0170.0000.0000.0000.000
211A237VAL0-0.046-0.01422.292-0.004-0.0040.0000.0000.0000.000
212A238HIS00.0450.05116.367-0.012-0.0120.0000.0000.0000.000
213A239TYR00.0570.00916.3560.0010.0010.0000.0000.0000.000
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